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112 lines
4.2 KiB
Org Mode
112 lines
4.2 KiB
Org Mode
#+TITLE: rorg --- R and org-mode
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* Objectives
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** Send data to R from org
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Org-mode includes orgtbl-mode, an extremely convenient way of using
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tabular data in a plain text file. Currently, spreadsheet
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functionality is available in org tables using the emacs package
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calc. It would be a boon both to org users and R users to allow
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org tables to be manipulated with the R programming language. Org
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tables give R users an easy way to enter and display data; R gives
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org users a powerful way to perform vector operations, statistical
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tests, and visualization on their tables.
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*** Implementations
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**** naive
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Naive implementation would be to use =(org-export-table "tmp.csv")=
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and =(ess-execute "read.csv('tmp.csv')")=.
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**** org-R
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org-R passes data to R from two sources: org tables, or csv
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files. Org tables are first exported to a temporary csv file
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using [[file:existing_tools/org-R.el::defun%20org%20R%20export%20to%20csv%20csv%20file%20options][org-R-export-to-csv]].
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**** org-exp-blocks
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**** RweaveOrg
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NA
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** evaluate R code from org and deal with output appropriately
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*** vector output
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When R code evaluation generates vectors and 2-dimensional arrays,
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this should be formatted appropriately in org buffers (orgtbl-mode) as well
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as in export targets (html, latex)
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**** Implementations
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***** org-R
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org-R converts R output (vectors, or matrices / 2d-arrays) to an
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org table and stores it in the org buffer, or in a separate org
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file (csv output would also be perfectly possible).
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***** org-exp-blocks
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***** RweaveOrg
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*** graphical output
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R can generate graphical output on a screen graphics device
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(e.g. X11, quartz), and in various standard image file formats
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(png, jpg, ps, pdf, etc). When graphical output is generated by
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evaluation of R code in Org, at least the following two things are desirable:
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1. output to screen for immediate viewing is possible
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2. graphical output to file is linked to appropriately from the
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org file This should have the automatic consequence that it is
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included appropriately in subsequent export targets (html,
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latex).
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**** Implementations
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***** org-R
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org-R does (1) if no output file is specified and (2) otherwise
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***** org-exp-blocks
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***** RweaveOrg
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* Notes
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** Special editing and evaluation of source code in R blocks
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Unfortunately org-mode how two different block types, both useful.
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In developing RweaveOrg, a third was introduced.
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Eric is leaning towards using the =#+begin_src= blocks, as that is
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really what these blocks contain: source code. Austin believes
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that specifying export options at the beginning of a block is
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useful functionality, to be preserved if possible.
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Note that upper and lower case are not relevant in block headings.
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*** Source code blocks
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Org has an extremely useful method of editing source code and
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examples in their native modes. In the case of R code, we want to
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be able to use the full functionality of ESS mode, including
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interactive evaluation of code.
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Source code blocks look like the following and allow for the
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special editing of code inside of the block through
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`org-edit-special'.
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#+BEGIN_SRC r
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,## hit C-c ' within this block to enter a temporary buffer in r-mode.
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,## while in the temporary buffer, hit C-c C-c on this comment to
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,## evaluate this block
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a <- 3
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a
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,## hit C-c ' to exit the temporary buffer
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#+END_SRC
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*** dblocks
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dblocks are useful because org-mode will automatically call
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`org-dblock-write:dblock-type' where dblock-type is the string
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following the =#+BEGIN:= portion of the line.
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dblocks look like the following and allow for evaluation of the
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code inside of the block by calling =\C-c\C-c= on the header of
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the block.
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#+BEGIN: dblock-type
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#+END:
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*** R blocks
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In developing RweaveOrg, Austin created [[file:existing_tools/RweaveOrg/org-sweave.el][org-sweave.el]]. This
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allows for the kind of blocks shown in [[file:existing_tools/RweaveOrg/testing.Rorg][testing.Rorg]]. These blocks
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have the advantage of accepting options to the Sweave preprocessor
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following the #+BEGIN_R declaration.
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* tasks
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* buffer dictionary
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LocalWords: DBlocks dblocks
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